Mitochondria’s Deviant Genetic Code: Evolution or Creation?

Before joining Reasons to Believe, I worked for nearly a decade in research and development (R&D) for a Fortune 500 company. During my tenure, on several occasions I was assigned to work on a “resurrected” project—one that was mothballed years earlier for one reason or another but was then deemed worthy of another go-around by upper management.

Of course, the first thing we did when we began work on the “old-project-made-new” was to review the work done by the previous R&D team. Invariably, we would come across things they had done that didn’t make sense to us whatsoever. I quickly learned that instead of deriding the previous team members for their questionable decision-making skills and flawed strategy, it was better to track down past team members and find out why they did things the way they did. Almost always, there were good reasons justifying their decisions. In fact, understanding their rationale often revealed an ingenuity to their approach.

The same can be said for mitochondria—bean-shaped organelles found in eukaryotic cells. Mitochondria play a crucial role in producing the energy that powers the cell’s operations. Based on a number of features possessed by these organelles—features that seemingly don’t make sense if mitochondria were created by a Divine Mind—many biologists believe that mitochondria have an evolutionary origin. Yet, as we learn more about mitochondria, scientists are discovering that the features that we thought made little sense from a creation model vantage point have a rationale for why they are the way they are. In fact, these features reflect an underlying ingenuity, as work by biochemists from Germany attests.1

We will take a look at the work of these biochemists later in this article. But first, it would be helpful to understand why evolutionary biologists think that the design of mitochondria makes no sense if these subcellular structures are to be understood as a Creator’s handiwork.

The Endosymbiont Hypothesis

Most evolutionary biologists believe the best explanation for the origin of mitochondria is the endosymbiont hypothesis. Lynn Margulis (1938–2011) advanced this idea to explain the origin of eukaryotic cells in the 1960s, building on the ideas of Russian botanist Konstantin Mereschkowsky.

Taught in introductory high school and college biology courses, Margulis’s work has become a cornerstone idea of the evolutionary paradigm. This classroom exposure explains why students often ask me about the endosymbiont hypothesis when I speak on university campuses. Many first-year biology students and professional life scientists alike find the evidence for the idea compelling and, consequently, view it as providing broad support for an evolutionary explanation for the history and design of life.

According to this hypothesis, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a “host” microbe. (Ingested cells that take up permanent residence within other cells are referred to as “endosymbionts.”)

Presumably, organelles such as mitochondria were once endosymbionts. Once taken into the host cell, the endosymbionts then took up permanent residency within the host, with the endosymbiont growing and dividing inside the host. Over time, the endosymbionts and the host became mutually interdependent, with the endosymbionts providing a metabolic benefit for the host cell. The endosymbionts gradually evolved into organelles through a process referred to as “genome reduction.” This reduction resulted when genes from the endosymbionts’ genomes were transferred into the genome of the host organism. Eventually, the host cell evolved the machinery to produce the proteins needed by the former endosymbiont and processes to transport those proteins into the organelle’s interior.

Evidence for the Endosymbiont Hypothesis

The similarities between organelles and bacteria serve as the main line of evidence for the endosymbiont hypothesis. For example, mitochondria—which are believed to be descended from a group of alphaproteobacteria—are about the same size and shape as a typical bacterium and have a double-membrane structure like these gram-negative cells. These organelles also divide in a way that is reminiscent of bacterial cells.

Biochemical evidence also exists for the endosymbiont hypothesis. Evolutionary biologists view the presence of the diminutive mitochondrial genome as a vestige of this organelle’s evolutionary history. Additionally, biologists view the biochemical similarities between mitochondrial and bacterial genomes as further evidence for the evolutionary origin of these organelles.

The presence of the unique lipid cardiolipin in the mitochondrial inner membrane also serves as evidence for the endosymbiont hypothesis. This is an important lipid component of bacterial inner membranes. Yet it is not found in the membranes of eukaryotic cells—except for in the inner membranes of mitochondria. In fact, biochemists consider it a signature lipid for mitochondria and a vestige of this organelle’s evolutionary history.

Does the Endosymbiont Hypothesis Successfully Account for the Origin of Mitochondria?

Despite the seemingly compelling evidence for the endosymbiont hypothesis, when researchers attempt to delineate the details of a presumed evolutionary transition, it becomes readily apparent that biologists lack a genuine explanation for the origin of mitochondria and, in a broader context, the origin of eukaryotic cells. In three previous articles, I detail some of the scientific challenges facing the endosymbiont hypothesis:

Given the scientific shortcomings of the endosymbiont hypothesis, is it reasonable to view mitochondria (and eukaryotic cells) as the work of a Creator?

I would maintain that it is. I argue that the shared similarities between mitochondria and alphaproteobacteria—which stand as the chief evidence for the endosymbiont hypothesis—reflect shared designs rather than a shared evolutionary history. It is common for human designers and engineers to reuse designs. So, why wouldn’t a Creator? See this article for more on this idea:

Why Do Mitochondria Have Their Own Genome and Cardiolipin in Their Inner Membranes?

However, to legitimately interpret the genesis of mitochondria from a creation model perspective, there must be a rationale for why mitochondria have their own diminutive genomes. And there has to be an explanation for why these organelles possess cardiolipin in their inner membranes, because on the surface, it appears as though mitochondrial genomes and cardiolipin are vestiges of the evolutionary history of these organelles.

As I have described previously (see the articles listed below), biochemists have recently learned that there are good reasons why mitochondria have their own genome—independent of the nuclear genome—and a sound rationale for the presence of cardiolipin in the inner membrane of these organelles. In other words, these features of mitochondria make sense from the vantage point of a creation model.

But, there is at least one other troubling feature of mitochondrial genomes that requires an explanation if we are to legitimately view these organelles as the handiwork of a Creator. For if they are a Creator’s handiwork, then why do mitochondria make use of deviant, nonuniversal genetic codes? Again, at first blush it would seem that the nonuniversal genetic code in mitochondria reflects their evolutionary origin. To understand why mitochondria have their own genetic code, a little background information is in order.

A Universal Genetic Code

The genetic code is a set of rules that define the information stored in DNA. These rules specify the sequence of amino acids that the cell’s machinery uses to build proteins. The genetic code consists of coding units, called “codons,” where each codon corresponds to one of the 20 amino acids found in proteins.

To a first approximation, all life on Earth possesses the same genetic code. To put it another way, the genetic code is universal. However, there are examples of organisms that possess a genetic code that deviates from the universal code in one or two of the coding assignments. Presumably, these deviant codes originate when the universal genetic code evolves, altering coding assignments.

The Deviant Genetic Codes of Mitochondria

Quite frequently, mitochondrial genomes employ deviant codes. One of the most common differences between the universal genetic code and the one found in mitochondrial genomes is the reassignment of one of the codons that specifies isoleucine (in the universal code) so that it specifies methionine. In fact, evolutionary biologists believe that this evolutionary transition happened five times in independent mitochondrial lineages.2

So, while many biologists believe that the nonuniversal genetic codes in mitochondria can be explained through evolutionary mechanisms, creationists (and ID proponents) must come up with a compelling reason for a Creator to alter the universal genetic code in the genome of these organelles. This issue becomes particularly pressing because biochemists have come to learn that the rules that define the genetic code are exquisitely optimized for error minimization (among other things), as I discuss in these articles:

So, is there a rationale for the reassignment of the isoleucine codon?

Work by a team of German biochemists provides an answer to this question—one that underscores an elegant molecular logic to the deviant genetic codes in mitochondria. These researchers provide evidence that the reassignment of the isoleucine codon for methionine protects proteins in the inner membrane of mitochondria from oxidative damage.

Metabolic reactions that take place in mitochondria during the energy harvesting process generate high levels of reactive oxygen species (ROS). These highly corrosive compounds will damage the lipids and the proteins of the mitochondrial inner membranes. The amino acid methionine is also readily oxidized by ROS to form methionine sulfoxide. Once this happens, the enzyme methionine sulfoxide reductase (MSR) reverses the oxidation reaction by reconverting the oxidized amino acid to methionine.

As a consequence of reassigning the isoleucine codon, methionine replaces isoleucine in the proteins encoded by the mitochondrial genome. Many of these proteins reside in the mitochondrial inner membrane. Interestingly, many of the isoleucine residues of the inner mitochondrial membrane proteins are located on the surfaces of the biomolecules. The replacement of isoleucine by methionine has minimal effect on the structure and function of these proteins because these two amino acids possess a similar size, shape, and hydrophobicity. But because methionine can react with ROS to form methionine sulfoxide and then be converted back to methionine by MSR, the mitochondrial inner membrane proteins and lipids are protected from oxidative damage. To put it another way, the codon reassignment results in a highly efficient antioxidant system for mitochondrial inner membranes.

The discovery of this antioxidant mechanism leads to another question: Why is the codon reassignment not universally found in the mitochondria of all organisms? As it turns out, the German biochemists discovered that this codon reassignment occurs in animals that are active, placing a high metabolic demand on mitochondria (and with it, concomitantly elevated production of ROS). On the other hand, this codon reassignment does not occur in Platyhelminthes (flatworms, which live without requiring oxygen) and inactive animals, such as sponges and echinoderms.

From a creation model vantage point, there are good reasons why things are the way they are regarding mitochondrial biochemistry. In fact, understanding the rationale for the design of mitochondria reveals an ingenuity to life’s designs.

As I have argued elsewhere, the seemingly independent evolutionary origin of identical (or nearly identical) biological features stands as a significant challenge to the evolutionary paradigm, while at the same time evincing a role for a Creator in the origin and history of life. For example, see my article “Like a Fish Out of Water: Why I’m Skeptical of the Evolutionary Paradigm.”

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